From ea704d688f62977735af7c2e6062c643d38537e0 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@broadinstitute.org>
Date: Sat, 15 Dec 2012 13:01:38 -0500
Subject: [PATCH] chose smaller buffer size for the bufferedStream

---
 .../sting/gatk/datasources/reads/GATKBAMIndex.java            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index c9cbdfb49..abaa0b226 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -69,7 +69,7 @@ public class GATKBAMIndex {
     private final File mFile;
 
     //TODO: figure out a good value for this buffer size
-    private final int BUFFERED_STREAM_BUFFER_SIZE=1024;
+    private final int BUFFERED_STREAM_BUFFER_SIZE=8192;
 
     /**
      * Number of sequences stored in this index.
@@ -303,7 +303,7 @@ public class GATKBAMIndex {
     private void openIndexFile() {
         try {
             fileStream = new SeekableFileStream(mFile);
-            bufferedStream = new SeekableBufferedStream(fileStream);
+            bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
         }
         catch (IOException exc) {
             throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc);